how to calculate UL throughput on the MAC level?

There are a few different ways I could take that question, with the most on-point probably being to look at the UL-SCH channel, and read 3GPP TS 36.321 as it relates to uplink data transfer by the UE.

In any case, I think something like this is better-asked in more mobile-centric message boards. There are a lot of strong protocol analysts on this site, and plenty of people who can answer virtually any question you'd have on Wireshark itself, but if you have a theory question on SC-FDMA you're not likely to find many mobile/RF experts here to answer it.

I would suggest checking out some of the 3GPP-related groups on Linkedin, as there's no shortage of radio experts there. eventhelix.com is a fairly good resource if you don't like navigating the 3GPP whitepapers; I wrote some of the EPC material they use, but I'm more of an authority on the core side and am definitely not an FDMA expert.

If you have access to logged LTE MAC PDUs (and you are asking on a Wireshark site), there are a couple of ways you can see the UL throughput. Depending upon your setup, it may be possible to query the eNodeB or test equipment for such statistics.

Assuming you have MAC PDUs, one way is to open the MAC Stats (Telephony | LTE | MAC) where there is a UL MBits/sec column. The time used is the time between first and last logged PDUs. There is also a tshark option to get the same information.

Another way is to plot an IO graph, which would let you see how it changes over time. With the Y Axis Units set to Advanced..., you can filter by mac-lte.ulsch (all UEs) or a specific UE (e.g. mac-lte.ueid == 10). The calculation would be SUM, and you probably want mac-lte.ulgrant-size (which is in bytes) as the field to plot. Note that this includes padding, which, depending upon how the MAC PDUs are logged, may not actually be present in the logged frame. Setting a long enough tick interval (say, 1 second) should give you a usable average.